It works! Thanks for Jason and Gustavo's replies.
Dongshan
On Tue, Jun 22, 2010 at 1:09 PM, Jason Swails <jason.swails.gmail.com> wrote:
> One thing I forgot to mention (though it's in the manual) -- this is only
> for the mdcrd (and probably mdvel if printed to) file, not the restart.
>
> All the best,
> Jason
>
> On Tue, Jun 22, 2010 at 1:08 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> See ntwprt variable in the amber manual. Only coordinates from atom number
>> 1 to ntwprt are printed, so if your solute appears at the beginning of your
>> prmtop, and the solute is, say 3000 atoms, then setting ntwprt=3000 will
>> cause only the solute to be printed.
>>
>> Hope this helps,
>> Jason
>>
>>
>> On Tue, Jun 22, 2010 at 12:16 PM, Dongshan Wei <dswei0523.gmail.com>wrote:
>>
>>> Hi All,
>>>
>>> I'm doing the explicit simulation of peptide folding in water, I need
>>> to save the trajectory in a high frequency (every ~0.2ps). If I save
>>> the trajectory of all atoms, the .mdcrd file will be very huge. So I
>>> just want to save the trajectory of ONLY the solute atoms (atoms of
>>> the peptide). Which command or which subroutine do I need to add or to
>>> modify?
>>>
>>> Thanks!
>>>
>>> Dongshan
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 22 2010 - 18:00:03 PDT
